2O9O

Crystal Structure of the buffalo Secretory Signalling Glycoprotein at 2.8 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ESC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.8298TRIS-HCL, NACL, 19% ETHANOL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.1α = 90
b = 66.859β = 90
c = 108.543γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray278IMAGE PLATEMARRESEARCHMIRROR2003-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.82097.10.12111134943
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.8595.50.432.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2ESC2.82011349108045451000.188520.188430.185720.23619RANDOM34.29
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-2.43-0.052.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg22.026
r_scangle_it4.874
r_scbond_it2.961
r_mcangle_it2.662
r_dihedral_angle_1_deg2.003
r_angle_refined_deg1.865
r_angle_other_deg1.594
r_mcbond_it1.441
r_nbtor_other0.778
r_symmetry_vdw_refined0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg22.026
r_scangle_it4.874
r_scbond_it2.961
r_mcangle_it2.662
r_dihedral_angle_1_deg2.003
r_angle_refined_deg1.865
r_angle_other_deg1.594
r_mcbond_it1.441
r_nbtor_other0.778
r_symmetry_vdw_refined0.59
r_symmetry_hbond_refined0.35
r_symmetry_vdw_other0.31
r_nbd_refined0.268
r_nbd_other0.252
r_xyhbond_nbd_refined0.157
r_chiral_restr0.119
r_xyhbond_nbd_other0.052
r_bond_refined_d0.019
r_gen_planes_refined0.007
r_gen_planes_other0.006
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2894
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing